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Oktavianthi S, Lages AC, Kusuma R, Kurniasih TS, Trimarsanto H, Andriani F, Rustandi D, Meriyanti T, Yusuf I, Malik SG, Jo J, Suriapranata I. Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia. Pathogens 2024; 13:279. [PMID: 38668234 PMCID: PMC11053823 DOI: 10.3390/pathogens13040279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/12/2024] [Accepted: 03/07/2024] [Indexed: 04/29/2024] Open
Abstract
The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 SARS-CoV-2 isolates collected from selected regions of Indonesia between January and October 2021 was performed to identify the distribution of SARS-CoV-2 variants and common mutations in Indonesia. During January-April 2021, Indonesian lineages B.1.466.2 and B.1.470 dominated, but from May 2021, Delta's AY.23 lineage outcompeted them. An analysis of 7515 published sequences from January 2021 to June 2022 revealed a decline in Delta in November 2021, followed by the emergence of Omicron variants in December 2021. We identified C241T (5'UTR), P314L (NSP12b), F106F (NSP3), and D614G (Spike) mutations in all sequences. The other common substitutions included P681R (76.4%) and T478K (60%) in Spike, D377Y in Nucleocapsid (61%), and I82T in Membrane (60%) proteins. Breakthrough infection and prolonged viral shedding cases were associated with Delta variants carrying the Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, and V1264L mutations. The dynamic of SARS-CoV-2 variants in Indonesia highlights the importance of continuous genomic surveillance in monitoring and identifying potential strains leading to disease outbreaks.
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Affiliation(s)
- Sukma Oktavianthi
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Aksar Chair Lages
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Rinaldy Kusuma
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Tri Shinta Kurniasih
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
- Menzies School of Health Research, Charles Darwin University, Darwin 0811, Australia
| | - Febi Andriani
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - David Rustandi
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Tandry Meriyanti
- Siloam Hospital Lippo Village, Tangerang 15810, Indonesia; (D.R.); (T.M.)
| | - Irawan Yusuf
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
| | - Safarina G. Malik
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia;
| | - Juandy Jo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
- Department of Biology, Faculty of Science and Technology, Universitas Pelita Harapan, Tangerang 15811, Indonesia
| | - Ivet Suriapranata
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia; (S.O.); (A.C.L.); (R.K.); (T.S.K.); (F.A.); (I.Y.); (S.G.M.); (J.J.)
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Bestari R, Nainggolan IRA, Hasibuan M, Ratnanggana R, Rahardjo K, Nastri AM, Dewantari JR, Soetjipto S, Lusida MI, Mori Y, Shimizu K, Kusumawati RL, Ichwan M, Lubis IND. SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia. IJID REGIONS 2023; 8:S1-S7. [PMID: 37799539 PMCID: PMC10548867 DOI: 10.1016/j.ijregi.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023]
Abstract
Objectives To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia. Methods A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument. Results Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.1.468 (n = 10), B.1 (n = 5), B.1.1 (n = 2), B.1.1.398 (n = 2), and B.6 (n = 1). Other unique amino acid mutations found in our samples were present in A58T on non-structural protein (NSP3) (70%), P323L on NSP12 (95%), Q57H on NS3 protein (75%), and D614G on S (100%). Conclusion The SARS-CoV-2 lineage B.1.468 may be the main virus variant circulating in North Sumatra at the beginning of the emergence of COVID-19 cases in this province.
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Affiliation(s)
- Ramadhan Bestari
- Faculty of Medicine, Universitas Islam Sumatera Utara, Medan, Indonesia
| | | | - Mirzan Hasibuan
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Rima Ratnanggana
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Krisnoadi Rahardjo
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | | | | | | | - Maria Inge Lusida
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Yasuko Mori
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Chuo-ku, Japan
| | - Kazufumi Shimizu
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Chuo-ku, Japan
| | - R Lia Kusumawati
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Muhammad Ichwan
- Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
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Balakrishnan KN, Yew CW, Chong ETJ, Daim S, Mohamad NE, Rodrigues K, Lee PC. Timeline of SARS-CoV-2 Transmission in Sabah, Malaysia: Tracking the Molecular Evolution. Pathogens 2023; 12:1047. [PMID: 37624007 PMCID: PMC10459040 DOI: 10.3390/pathogens12081047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic poses an unprecedented public health challenge in Malaysia. The impact of COVID-19 varies between countries, including geographically divided states within a country. The deadly transmission of COVID-19 has taken a heavy toll in Sabah, Malaysia's third most populous state, contributing nearly 10% to the recorded national death toll as of 31 December 2022. Although several SARS-CoV-2 genome sequences have been analysed in Malaysia, molecular epidemiology data from Sabah focusing on the diversity and evolution of SARS-CoV-2 variants are still lacking. This study examines the major SARS-CoV-2 variants and emerging mutations from Sabah, the Malaysian Borneo, which is geographically divided from West Malaysia by the South China Sea. METHODS A total of 583 COVID-19 samples were subjected to whole genome sequencing and analysed with an additional 1123 Sabah COVID-19 sequences retrieved from the GISAID EpiCoV consortium. Nextclade and Pangolin were used to classify these sequences according to the clades and lineages. To determine the molecular evolutionary characteristics, Bayesian time-scaled phylogenetic analysis employing the maximum likelihood algorithm was performed on selected SARS-CoV-2 genome sequences, using the Wuhan-Hu-1 sequence as a reference. RESULTS Sabah was affected starting from the second COVID-19 wave in Malaysia, and the early sequences were classified under the O clade. The clade was gradually replaced during subsequent waves by G, GH, GK and GRA, with the latter being dominant as of December 2022. Phylogenetically, the Delta isolates in this study belong to the three main subclades 21A, 21J and 21I, while Omicron isolates belong to 21M, 21L and 22B. The time-scaled phylogeny suggested that SARS-CoV-2 introduced into Sabah originated from Peninsular Malaysia in early March 2020, and phylodynamic analysis indicated that increased viral spread was observed in early March and declined in late April, followed by an evolutionary stationary phase in June 2020. CONCLUSION Continuous molecular epidemiology of SARS-CoV-2 in Sabah will provide a deeper understanding of the emergence and dominance of each variant in the locality, thus facilitating public health intervention measures.
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Affiliation(s)
- Krishnan Nair Balakrishnan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Chee Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Eric Tzyy Jiann Chong
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Sylvia Daim
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Nurul Elyani Mohamad
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Kenneth Rodrigues
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Ping-Chin Lee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
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Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND. Toward a global virus genomic surveillance network. Cell Host Microbe 2023; 31:861-873. [PMID: 36921604 PMCID: PMC9986120 DOI: 10.1016/j.chom.2023.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest a generalizable modular sequencing framework wherein users can easily switch between virus targets to maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic surveillance would aid control programs and potentially provide a warning system for outbreaks, using a global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as examples.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA; The Rockefeller Foundation, New York, NY, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
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Rahadi DA, Yusri E, Putra SP, Semiarty R, Pertiwi D, Ilmiawati C. COVID-19 Vaccination and Clinical Outcomes at a Secondary Referral Hospital During the Delta Variant-dominant Period in West Sumatra, Indonesia. J Prev Med Public Health 2023; 56:221-230. [PMID: 37287199 DOI: 10.3961/jpmph.23.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/20/2023] [Indexed: 06/09/2023] Open
Abstract
OBJECTIVES The second wave of coronavirus disease 2019 (COVID-19) cases in Indonesia, during which the Delta variant predominated, took place after a vaccination program had been initiated in the country. This study was conducted to assess the impact of COVID-19 vaccination on unfavorable clinical outcomes including hospitalization, severe COVID-19, intensive care unit (ICU) admission, and death using a real-world model. METHODS This single-center retrospective cohort study involved patients with COVID-19 aged ≥18 years who presented to the COVID-19 emergency room at a secondary referral teaching hospital between June 1, 2021 and August 31, 2021. We used a binary logistic regression model to assess the effect of COVID-19 vaccination on unfavorable clinical outcomes, with age, sex, and comorbidities as confounding variables. RESULTS A total of 716 patients were included, 32.1% of whom were vaccinated. The elderly participants (≥65 years) had the lowest vaccine coverage among age groups. Vaccination had an effectiveness of 50% (95% confidence interval [CI], 25 to 66) for preventing hospitalization, 97% (95% CI, 77 to 99) for preventing severe COVID-19, 95% (95% CI, 56 to 99) for preventing ICU admission, and 90% (95% CI, 22 to 99) for preventing death. Interestingly, patients with type 2 diabetes had a 2-fold to 4-fold elevated risk of unfavorable outcomes. CONCLUSIONS Among adults, COVID-19 vaccination has a moderate preventive impact on hospitalization but a high preventive impact on severe COVID-19, ICU admission, and death. The authors suggest that relevant parties increase COVID-19 vaccination coverage, especially in the elderly population.
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Affiliation(s)
- Didan Ariadapa Rahadi
- Undergraduate Program of Medicine, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
| | - Elfira Yusri
- Department of Clinical Pathology, Undergraduate Program of Medicine, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
| | - Syandrez Prima Putra
- Department of Microbiology, Undergraduate Program of Medicine, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
- Center for Infectious Disease Diagnostic and Research (PDRPI), Faculty of Medicine, Universitas Andalas, Padang, Indonesia
| | - Rima Semiarty
- Department of Public Health, Undergraduate Program of Medicine, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
- Doctoral Program of Public Health, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
| | - Dian Pertiwi
- Department of Clinical Pathology, Undergraduate Program of Medicine, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
| | - Cimi Ilmiawati
- Doctoral Program of Public Health, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
- Department of Pharmacology, Undergraduate Program of Medicine, Faculty of Medicine, Universitas Andalas, Padang, Indonesia
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Sequence analysis of SARS-CoV-2 Delta variant isolated from Makassar, South Sulawesi, Indonesia. Heliyon 2023; 9:e13382. [PMID: 36744069 PMCID: PMC9886429 DOI: 10.1016/j.heliyon.2023.e13382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/01/2023] Open
Abstract
Introduction This study aimed to perform mutation and phylogenetic analyses of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Delta variants and analyze the characteristic signs and symptoms of patients infected with SARS-CoV-2 Delta variant originated from Makassar during the Delta outbreak.Methods: We collected samples from patients who were infected with coronavirus disease 2019 (COVID-19) between June and October 2021. We selected the Quantitative Reverse Transcription-Polymerase Chain Reaction (PCR)-positive samples with a cycle threshold value of <30 for whole genome sequencing. Total viral ribonucleic acid (RNA) was isolated from 34 PCR-positive nasopharyngeal swab samples, and whole genome sequencing was performed using the Oxford Nanopore GridlON sequencer. Phylogenetic and maximum clade credibility analyses were performed using the Bayesian Markov chain Monte Carlo method. Results It was found that 33 patients were infected with the SARS-CoV-2 Delta variant in this cohort study, among whom 63.6% (21) patients were female. According to the clinical data, 24 (72.7%), 7 (21.2%), and 2 (6.1%) patients had mild, moderate, and severe COVID-19 infections. Phylogenetic analysis based on the spike and RNA-dependent RNA polymerase (RdRp) genes showed that the collected samples were clustered in the main lineage of B.1.617.2 (Delta variant). The Delta variants had a high frequency of distinct mutations in the spike protein region, including T19R (94.12%), L452R (88.23%), T478K (91.17%), D614G (97%), P681R (97%), and D950 N (97%). Other unique mutations found in a smaller frequency in our samples were present in the N-terminal domain, including A27T (2.94%) and A222V (14.70%), and in the receptor-binding domain, including Q414K (5.88%), G446V (2.94%), and T470 N (2.94%). Conclusion This study revealed the unique mutations in the S protein region of Delta variants. T19R, L452R, T478K/T478R, D614G, P681R, and D950 N were the most common substitutions in Makassar's Delta variant.
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Azami NAM, Perera D, Thayan R, AbuBakar S, Sam IC, Salleh MZ, Isa MNM, Ab Mutalib NS, Aik WK, Suppiah J, Tan KK, Chan YF, Teh LK, Azzam G, Rasheed ZBM, Chan JCJ, Kamel KA, Tan JY, Khalilur Rahman O, Lim WF, Johari NA, Ishak M, Yunos RIM, Anasir MI, Wong JE, Fu JYL, Noorizhab MNF, Sapian IS, Mokhtar MFM, Md Shahri NAA, Ghafar K, Yusuf SNHM, Noor YM, Jamal R. SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave. Int J Infect Dis 2022; 125:216-226. [PMID: 36336246 PMCID: PMC9632236 DOI: 10.1016/j.ijid.2022.10.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/25/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program. METHODS COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle threshold values <30 were obtained throughout Malaysia. Sequencing of SARS-CoV-2 complete genomes was performed using Illumina, Oxford Nanopore, or Ion Torrent platforms. A total of 6163 SARS-CoV-2 complete genome sequences were generated over the surveillance period. All sequences were submitted to the Global Initiative on Sharing All Influenza Data database. RESULTS From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern, including the original B.1.617.2 lineage and descendant AY lineages. The B.1.617.2 lineage was identified as the early dominant circulating strain throughout the country but over time, was displaced by AY.59 and AY.79 lineages in Peninsular (west) Malaysia, and the AY.23 lineage in east Malaysia. In December 2021, pilgrims returning from Saudi Arabia facilitated the introduction and spread of the BA.1 lineage (Omicron variant of concern) in the country. CONCLUSION The changing trends of circulating SARS-CoV-2 lineages were identified, with differences observed between west and east Malaysia. This initiative highlighted the importance of leveraging research expertise in the country to facilitate pandemic response and preparedness.
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Affiliation(s)
- Nor Azila Muhammad Azami
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | - David Perera
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Ravindran Thayan
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia; Department of Medical Microbiology, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Mohd Noor Mat Isa
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
| | - Nurul Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | - Wong Kiing Aik
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Jeyanthi Suppiah
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Kim-Kee Tan
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Ghows Azzam
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Jonathan Chia Jui Chan
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Khayri Azizi Kamel
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Jia-Yi Tan
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Omar Khalilur Rahman
- Department of Medical Microbiology, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Wai Feng Lim
- Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Nor Azfa Johari
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
| | - Muhiddin Ishak
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | - Ryia Illani Mohd Yunos
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | - Mohd Ishtiaq Anasir
- Virology Unit, Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Selangor, Malaysia
| | - Jo-Ern Wong
- Tropical Infectious Diseases Research & Education Centre (TIDREC), Higher Institution Center of Excellence (HICoE), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Jolene Yin Ling Fu
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Mohd Nur Fakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute, Universiti Teknologi Mara (UiTM) Selangor Branch, Puncak Alam Campus, Selangor, Malaysia
| | - Irni Suhayu Sapian
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
| | | | | | - Khairun Ghafar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia
| | | | - Yusuf Muhammad Noor
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Selangor, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur, Malaysia.
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A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains. Genes (Basel) 2022; 13:genes13081330. [PMID: 35893066 PMCID: PMC9394340 DOI: 10.3390/genes13081330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 02/04/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly emerging virus well known as the major cause of the worldwide pandemic due to Coronavirus Disease 2019 (COVID-19). Major breakthroughs in the Next Generation Sequencing (NGS) field were elucidated following the first release of a full-length SARS-CoV-2 genome on the 10 January 2020, with the hope of turning the table against the worsening pandemic situation. Previous studies in respiratory virus characterization require mapping of raw sequences to the human genome in the downstream bioinformatics pipeline as part of metagenomic principles. Illumina, as the major player in the NGS arena, took action by releasing guidelines for improved enrichment kits called the Respiratory Virus Oligo Panel (RVOP) based on a hybridization capture method capable of capturing targeted respiratory viruses, including SARS-CoV-2; therefore, allowing a direct map of raw sequences data to SARS-CoV-2 genome in downstream bioinformatics pipeline. Consequently, two bioinformatics pipelines emerged with no previous studies benchmarking the pipelines. This study focuses on gaining insight and understanding of target enrichment workflow by Illumina through the utilization of different bioinformatics pipelines named as 'Fast Pipeline' and 'Normal Pipeline' to SARS-CoV-2 strains isolated from Yogyakarta and Central Java, Indonesia. Overall, both pipelines work well in the characterization of SARS-CoV-2 samples, including in the identification of major studied nucleotide substitutions and amino acid mutations. A higher number of reads mapped to the SARS-CoV-2 genome in Fast Pipeline and merely were discovered as a contributing factor in a higher number of coverage depth and identified variations (SNPs, insertion, and deletion). Fast Pipeline ultimately works well in a situation where time is a critical factor. On the other hand, Normal Pipeline would require a longer time as it mapped reads to the human genome. Certain limitations were identified in terms of pipeline algorithm, whereas it is highly recommended in future studies to design a pipeline in an integrated framework, for instance, by using NextFlow, a workflow framework to combine all scripts into one fully integrated pipeline.
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Zhu M, Zeng Q, Saputro BIL, Chew SP, Chew I, Frendy H, Tan JW, Li L. Tracking the molecular evolution and transmission patterns of SARS-CoV-2 lineage B.1.466.2 in Indonesia based on genomic surveillance data. Virol J 2022; 19:103. [PMID: 35710544 PMCID: PMC9202327 DOI: 10.1186/s12985-022-01830-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/02/2022] [Indexed: 12/22/2022] Open
Abstract
Background As a new epi-center of COVID-19 in Asia and a densely populated developing country, Indonesia is facing unprecedented challenges in public health. SARS-CoV-2 lineage B.1.466.2 was reported to be an indigenous dominant strain in Indonesia (once second only to the Delta variant). However, it remains unclear how this variant evolved and spread within such an archipelagic nation. Methods For statistical description, the spatiotemporal distributions of the B.1.466.2 variant were plotted using the publicly accessible metadata in GISAID. A total of 1302 complete genome sequences of Indonesian B.1.466.2 strains with high coverage were downloaded from the GISAID’s EpiCoV database on 28 August 2021. To determine the molecular evolutionary characteristics, we performed a time-scaled phylogenetic analysis using the maximum likelihood algorithm and called the single nucleotide variants taking the Wuhan-Hu-1 sequence as reference. To investigate the spatiotemporal transmission patterns, we estimated two dynamic parameters (effective population size and effective reproduction number) and reconstructed the phylogeography among different islands. Results As of the end of August 2021, nearly 85% of the global SARS-CoV-2 lineage B.1.466.2 sequences (including the first one) were obtained from Indonesia. This variant was estimated to account for over 50% of Indonesia’s daily infections during the period of March–May 2021. The time-scaled phylogeny suggested that SARS-CoV-2 lineage B.1.466.2 circulating in Indonesia might have originated from Java Island in mid-June 2020 and had evolved into two disproportional and distinct sub-lineages. High-frequency non-synonymous mutations were mostly found in the spike and NSP3; the S-D614G/N439K/P681R co-mutations were identified in its larger sub-lineage. The demographic history was inferred to have experienced four phases, with an exponential growth from October 2020 to February 2021. The effective reproduction number was estimated to have reached its peak (11.18) in late December 2020 and dropped to be less than one after early May 2021. The relevant phylogeography showed that Java and Sumatra might successively act as epi-centers and form a stable transmission loop. Additionally, several long-distance transmission links across seas were revealed. Conclusions SARS-CoV-2 variants circulating in the tropical archipelago may follow unique patterns of evolution and transmission. Continuous, extensive and targeted genomic surveillance is essential. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01830-1.
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Affiliation(s)
- Mingjian Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianli Zeng
- Shanghai Institute of Biological Products, Shanghai, China
| | | | - Sien Ping Chew
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ian Chew
- Zhejiang University School of Medicine, Hangzhou, China
| | - Holie Frendy
- Faculty of Medicine and Health Sciences, Krida Wacana Christian University, Jakarta, Indonesia
| | - Joanna Weihui Tan
- Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Palou T, Wilmot M, Duchene S, Porter A, Kemoi MJ, Suarkia D, Andersson P, Watt A, Sherry N, Seemann T, Sait M, Turharus C, Nguyen S, Schlebusch S, Thompson C, McMahon J, Vaccher S, Lin C, Daoni E, Howden BP, Susapu M. Genomic Characterisation Reveals a Dominant Lineage of SARS-CoV-2 in Papua New Guinea. Virus Evol 2022; 8:veac033. [PMID: 35875697 PMCID: PMC9278129 DOI: 10.1093/ve/veac033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/22/2022] [Accepted: 04/01/2022] [Indexed: 11/14/2022] Open
Abstract
The coronavirus disease pandemic has highlighted the utility of pathogen genomics as a
key part of comprehensive public health response to emerging infectious diseases threats,
however, the ability to generate, analyse, and respond to pathogen genomic data varies
around the world. Papua New Guinea (PNG), which has limited in-country capacity for
genomics, has experienced significant outbreaks of severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) with initial genomics data indicating a large proportion of
cases were from lineages that are not well defined within the current nomenclature.
Through a partnership between in-country public health agencies and academic
organisations, industry, and a public health genomics reference laboratory in Australia a
system for routine SARS-CoV-2 genomics from PNG was established. Here we aim to
characterise and describe the genomics of PNG’s second wave and examine the sudden
expansion of a lineage that is not well defined but very prevalent in the Western Pacific
region. We generated 1797 sequences from cases in PNG and performed phylogenetic and
phylodynamic analyses to examine the outbreak and characterise the circulating lineages
and clusters present. Our results reveal the rapid expansion of the B.1.466.2 and related
lineages within PNG, from multiple introductions into the country. We also highlight the
difficulties that unstable lineage assignment causes when using genomics to assist with
rapid cluster definitions.
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Affiliation(s)
- Theresa Palou
- National Control Centre, Ministry of Health, Papua New Guinea
| | - Mathilda Wilmot
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ashleigh Porter
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ms Janlyn Kemoi
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | | | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anne Watt
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - Son Nguyen
- Forensic and Scientific Services, Queensland Health, Brisbane, Australia
| | | | - Craig Thompson
- Forensic and Scientific Services, Queensland Health, Brisbane, Australia
| | - Jamie McMahon
- Forensic and Scientific Services, Queensland Health, Brisbane, Australia
| | | | - Chantel Lin
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Esorom Daoni
- National Control Centre, Ministry of Health, Papua New Guinea
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Melinda Susapu
- National Control Centre, Ministry of Health, Papua New Guinea
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